ArticleNucleic acids research2022
SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 40 citations in OpenAlex.
- Single-cell profiling and genetic regulation of alternative polyadenylation in the human brain.Nature genetics · 2026Article
- Benchmarking computational methods for identifying and quantifying polyadenylation sites from 3' tag-based single-cell RNA-seq data.Nucleic acids research · 2026Article
- Accurate profiling of single-cell alternative transcript start sites by correcting RNA degradation.Nature communications · 2026Article
- Experimental and computational methods for allelic imbalance analysis from single-nucleus RNA-seq data.Genome biology · 2026Article
- miRNA regulation in brain tissue space: the 3'UTR perspective.RNA (New York, N.Y.) · 2026Review
- Alternative polyadenylation links RNA processing to iron metabolism in human erythropoiesis.Nucleic acids research · 2026Article
- Global mRNA 3'UTR lengthening in small-cell neuroendocrine carcinoma.bioRxiv : the preprint server for biology · 2026Article
- Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.Lipids in health and disease · 2026Article
- metaAPA: a tool for integration of PolyA site predictions from single-cell and spatial transcriptomics.Bioinformatics advances · 2026Article
- CpG Methylation-Driven Pleiotropic Spliced Isoforms of PRSS3 Facilitate Gastric Intratumor Heterogeneity and Metastasis.Cancer science · 2026Article
- Glioblastoma exploits ATP from leading-edge astrocytes to fuel its infiltrative growth revealed by spatially resolved chimeric analysis.Science advances · 2025Article
- Multitissue single-nucleus RNA-seq reveals cell type-specific regulatory patterns of alternative polyadenylation in pigs.Genome research · 2025Article
- scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3' scRNA-seq data.Genome biology · 2025Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Unveiling cell-type-specific microRNA networks through alternative polyadenylation in glioblastoma.BMC biology · 2025Article
- RNA-binding proteins regulate osteoarthritis via RNA metabolism regulation.Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences · 2024Review
- Supervised analysis of alternative polyadenylation from single-cell and spatial transcriptomics data with spvAPA.Briefings in bioinformatics · 2024Article
- Alternative polyadenylation-related genetic variants contribute to bladder cancer risk.Journal of biomedical research · 2023Article
- Infernape uncovers cell type-specific and spatially resolved alternative polyadenylation in the brain.Genome research · 2023Article
- Trackplot: A flexible toolkit for combinatorial analysis of genomic data.PLoS computational biology · 2023Article
Corrections and comments
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Authors and funding
17 authors at 2 institutions in 3 countries.
Funding
Abstract
Alternative polyadenylation increases transcript diversities at the 3' end, regulating biological processes including cell differentiation, embryonic development and cancer progression. Here, we present a Bayesian method SCAPE, which enables de novo identification and quantification of polyadenylation (pA) sites at single-cell level by utilizing insert size information. We demonstrated its accuracy and robustness and identified 31 558 sites from 36 mouse organs, 43.8% (13 807) of which were novel. We illustrated that APA isoforms were associated with miRNAs binding and regulated in tissue-, cell type-and tumor-specific manners where no difference was found at gene expression level, providing an extra layer of information for cell clustering. Furthermore, we found genome-wide dynamic changes of APA usage during erythropoiesis and induced pluripotent stem cell (iPSC) differentiation, suggesting APA contributes to the functional flexibility and diversity of single cells. We expect SCAPE to aid the analyses of cellular dynamics and diversities in health and disease.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.